Clinical characteristics distributions on TMA36 cohort

Clinical characteristics distributions by CANARY

Good prognosis (Indolent)

Intermediate prognosis

Poor prognosis (Aggressive)

Clinical characteristics distributions by SILA Score

## Using CANARY as id variables
## Warning in wilcox.test.default(c(0.049, 0.115, 0.23, 0.315, 0.322, 0.274, :
## cannot compute exact p-value with ties

## Using Stages_simplified as id variables

## Using Hist_predominant as id variables

## Using Death_st as id variables

## Using Recurrence_st as id variables

## Using Progression_st as id variables

## Using Smoking_Status as id variables

New classification

Identifying outliers

pt_ID SILA CANARY Stages_simplified X8th_ed_path_stage Hist_predominant Hist_other_patterns Death_st Recurrence_st Progression_st
1 7984 0.049 G Stage I Stage IA1 solid acinar, lepidic No Yes Yes
54 13634 0.250 G Stage III Stage IIIB solid NA No No No
78 14958 0.148 G Stage I Stage IB solid acinar No No No
9 11652 0.479 I Stage I Stage IA1 papillary micropapillary No Yes No
10 11728 0.408 I Stage I Stage IA2 micropapillary acinar, solid No No No
21 11918 0.360 I Stage I Stage IA1 solid acinar, lepidic No No No
28 12546 0.476 I Stage I Stage IA1 papillary acinar Yes No No
36 12935 0.441 I Stage IV Stage IV solid NA Yes No Yes
26 12281 0.340 P Stage I Stage IA2 acinar lepidic, micropapillary No No No

Option 1: Indolent < 0.5 | Aggressive >= 0.5

Indolent as SILA < 0.5

pt_ID SILA CANARY Stages_simplified X8th_ed_path_stage Hist_predominant Hist_other_patterns Death_st Recurrence_st Progression_st
1 7984 0.049 G Stage I Stage IA1 solid acinar, lepidic No Yes Yes
2 8356 0.115 G Stage 0 Stage 0 lepidic NA No No No
4 11522 0.230 G Stage I Stage IA3 acinar lepidic No No No
9 11652 0.479 I Stage I Stage IA1 papillary micropapillary No Yes No
10 11728 0.408 I Stage I Stage IA2 micropapillary acinar, solid No No No
16 11851 0.428 I Stage I Stage IB acinar NA No No No
18 11886 0.315 G Stage I Stage IB acinar solid No No No
21 11918 0.360 I Stage I Stage IA1 solid acinar, lepidic No No No
22 11938 0.417 I Stage I Stage IB acinar lepidic No No No
26 12281 0.340 P Stage I Stage IA2 acinar lepidic, micropapillary No No No
28 12546 0.476 I Stage I Stage IA1 papillary acinar Yes No No
31 12911 0.322 G Stage I Stage IA2 acinar micropapillary, lepidic No No No
32 12915 0.435 I Stage I Stage IB acinar lepidic No No No
36 12935 0.441 I Stage IV Stage IV solid NA Yes No Yes
40 13055 0.418 I Stage I Stage IA3 acinar micropapillary No No No
45 13276 0.459 I Stage I Stage IA2 acinar micropapillary No No No
48 13376 0.274 G Stage I Stage IB lepidic acinar No No No
51 13538 0.368 I Stage I Stage IA1 papillary lepidic No No No
54 13634 0.250 G Stage III Stage IIIB solid NA No No No
63 13922 0.359 I Stage II Stage IIB acinar solid No No No
66 14201 0.416 I Stage I Stage IA2 acinar lepidic No No No
69 14428 0.493 I Stage I Stage IA2 acinar micropapillary, lepidic No No No
72 14825 0.418 I Stage II Stage IIB acinar micropapillary No No No
78 14958 0.148 G Stage I Stage IB solid acinar No No No
80 14965 0.350 G Stage I Stage IA3 acinar lepidic No No No
83 15083 0.421 I Stage I Stage IA2 acinar micropapillary, lepidic No No No
92 15641 0.380 I Stage II Stage IIB acinar solid, micropapillary No No No
93 15741 0.405 I Stage I Stage IA2 acinar lepidic No No No

Aggressive as SILA >= 0.5

pt_ID SILA CANARY Stages_simplified X8th_ed_path_stage Hist_predominant Hist_other_patterns Death_st Recurrence_st Progression_st
3 11424 0.750 P Stage I Stage IA3 solid NA No No No
5 11538 0.758 P Stage I Stage IB micropapillary NA No Yes No
6 11561 0.555 P Stage I Stage IA3 papillary acinar, micropapillary No No No
7 11601 0.610 P Stage I Stage IA1 solid acinar No No No
8 11646 0.695 P Stage I Stage IA2 micropapillary solid, acinar No No No
11 11759 0.634 P Stage I Stage IA2 acinar micropapillary No No No
12 11813 0.547 P Stage I Stage IA2 acinar lepidic No No No
13 11817 0.797 P Stage II Stage IIB acinar solid Yes Yes Yes
14 11820 0.665 P Stage I Stage IA1 acinar solid No No No
15 11840 0.596 P Stage I Stage IA3 solid acinar No Yes Yes
17 11855 0.761 P Stage I Stage IA3 acinar NA No No No
19 11901 0.647 P Stage I Stage IA3 acinar solid Yes No No
20 11906 0.505 I Stage I Stage IA2 acinar lepidic No No No
23 11952 0.822 P Stage I Stage IA3 acinar NA No No No
24 11957 0.712 P Stage III Stage IIIA acinar solid Yes No No
25 12177 0.649 P Stage III Stage IIIA acinar solid Yes No Yes
27 12323 0.794 P Stage III Stage IIIA acinar micropapillary No No No
29 12889 0.768 P Stage II Stage IIB solid NA No No No
30 12890 0.791 P Stage II Stage IIA acinar micropapillary Yes No Yes
33 12924 0.669 P Stage II Stage IIB papillary acinar Yes Yes No
34 12929 0.622 P Stage II Stage IIB acinar lepidic Yes No Yes
35 12931 0.790 P Stage II Stage IIA solid acinar No No No
37 12994 0.750 P Stage III Stage IIIB micropapillary acinar Yes No Yes
38 13014 0.735 P Stage II Stage IIA acinar micropapillary No No No
39 13034 0.551 P Stage I Stage IB micropapillary acinar No No Yes
41 13074 0.742 P Stage I Stage IA2 solid acinar Yes No Yes
42 13155 0.731 P Stage I Stage IA3 acinar micropappilary No No No
43 13197 0.697 P Stage II Stage IIB acinar micropapillary No No No
44 13207 0.675 P Stage I Stage IA3 micropapillary NA No No No
46 13317 0.697 P Stage I Stage IA3 micropapillary solid No No No
47 13356 0.621 P Stage II Stage IIB acinar solid Yes No No
49 13436 0.739 P Stage II Stage IIB acinar NA No No No
50 13536 0.502 I Stage I Stage IA2 acinar NA No No No
52 13579 0.664 P Stage II Stage IIB acinar NA No No No
53 13622 0.799 P Stage II Stage IIA solid NA No No No
55 13636 0.853 P Stage III Stage IIIA papillary NA No No No
56 13651 0.548 P Stage III Stage IIIA acinar lepidic No No No
57 13724 0.789 P Stage II Stage IIA solid acinar No Yes Yes
58 13746 0.821 P Stage IV Stage IV acinar NA No No Yes
59 13769 0.699 P Stage II Stage IIA acinar lepidic No No No
60 13771 0.554 P Stage I Stage IA3 papillary acinar No No No
61 13774 0.735 P Stage I Stage IA3 acinar papillary Yes Yes Yes
62 13801 0.705 P Stage I Stage IA2 acinar NA Yes No No
64 13988 0.575 P Stage II Stage IIA acinar NA No No No
65 14048 0.774 P Stage I Stage IB acinar NA Yes No No
67 14301 0.826 P Stage II Stage IIB micropapillary solid, acinar No No No
68 14330 0.732 P Stage II Stage IIA acinar lepidc No No No
70 14610 0.758 P Stage II Stage IIA mucinous acinar lepidic No No No
71 14813 0.627 P Stage I Stage IA2 solid acinar, lepidic No No No
73 14836 0.773 P Stage I Stage IA3 solid acinar No No No
74 14855 0.513 I Stage I Stage IB acinar micropapillary No No No
75 14933 0.599 P Stage I Stage IA3 acinar micropapillary No Yes No
76 14953 0.821 P Stage II Stage IIA solid NA No No No
77 14955 0.560 P Stage II Stage IIB solid acinar No No No
79 14962 0.721 P Stage II Stage IIB papillary acinar No No No
81 15001 0.532 I Stage I Stage IB micropapillary acinar No No No
82 15002 0.724 P Stage II Stage IIA solid NA No No No
84 15187 0.616 P Stage I Stage IA2 acinar lepidic No No No
85 15224 0.716 P Stage I Stage IA2 acinar papillary, micropapillary No No No
86 15325 0.622 P Stage I Stage IA1 papillary NA No No No
87 15326 0.612 P Stage I Stage IA3 acinar micropapillary No No No
88 15467 0.699 P Stage I Stage IA3 mucinous acinar NA No No No
89 15506 0.777 P Stage II Stage IIA mucinous acinar NA No No No
90 15569 0.687 P Stage II Stage IIA acinar solid No No No
91 15626 0.699 P Stage II Stage IIB acinar micropapilary, papillary, lepidic No No Yes

Option 2: Indolent < 0.4 | intermediate > 0.4 <= 0.6 | Aggressive > 0.6

Indolent as SILA <= 0.4

pt_ID SILA CANARY Stages_simplified X8th_ed_path_stage Hist_predominant Hist_other_patterns Death_st Recurrence_st Progression_st
1 7984 0.049 G Stage I Stage IA1 solid acinar, lepidic No Yes Yes
2 8356 0.115 G Stage 0 Stage 0 lepidic NA No No No
4 11522 0.230 G Stage I Stage IA3 acinar lepidic No No No
18 11886 0.315 G Stage I Stage IB acinar solid No No No
21 11918 0.360 I Stage I Stage IA1 solid acinar, lepidic No No No
26 12281 0.340 P Stage I Stage IA2 acinar lepidic, micropapillary No No No
31 12911 0.322 G Stage I Stage IA2 acinar micropapillary, lepidic No No No
48 13376 0.274 G Stage I Stage IB lepidic acinar No No No
51 13538 0.368 I Stage I Stage IA1 papillary lepidic No No No
54 13634 0.250 G Stage III Stage IIIB solid NA No No No
63 13922 0.359 I Stage II Stage IIB acinar solid No No No
78 14958 0.148 G Stage I Stage IB solid acinar No No No
80 14965 0.350 G Stage I Stage IA3 acinar lepidic No No No
92 15641 0.380 I Stage II Stage IIB acinar solid, micropapillary No No No

Intermediate as SILA > 0.4 <= 0.6

pt_ID SILA CANARY Stages_simplified X8th_ed_path_stage Hist_predominant Hist_other_patterns Death_st Recurrence_st Progression_st
6 11561 0.555 P Stage I Stage IA3 papillary acinar, micropapillary No No No
9 11652 0.479 I Stage I Stage IA1 papillary micropapillary No Yes No
10 11728 0.408 I Stage I Stage IA2 micropapillary acinar, solid No No No
12 11813 0.547 P Stage I Stage IA2 acinar lepidic No No No
15 11840 0.596 P Stage I Stage IA3 solid acinar No Yes Yes
16 11851 0.428 I Stage I Stage IB acinar NA No No No
20 11906 0.505 I Stage I Stage IA2 acinar lepidic No No No
22 11938 0.417 I Stage I Stage IB acinar lepidic No No No
28 12546 0.476 I Stage I Stage IA1 papillary acinar Yes No No
32 12915 0.435 I Stage I Stage IB acinar lepidic No No No
36 12935 0.441 I Stage IV Stage IV solid NA Yes No Yes
39 13034 0.551 P Stage I Stage IB micropapillary acinar No No Yes
40 13055 0.418 I Stage I Stage IA3 acinar micropapillary No No No
45 13276 0.459 I Stage I Stage IA2 acinar micropapillary No No No
50 13536 0.502 I Stage I Stage IA2 acinar NA No No No
56 13651 0.548 P Stage III Stage IIIA acinar lepidic No No No
60 13771 0.554 P Stage I Stage IA3 papillary acinar No No No
64 13988 0.575 P Stage II Stage IIA acinar NA No No No
66 14201 0.416 I Stage I Stage IA2 acinar lepidic No No No
69 14428 0.493 I Stage I Stage IA2 acinar micropapillary, lepidic No No No
72 14825 0.418 I Stage II Stage IIB acinar micropapillary No No No
74 14855 0.513 I Stage I Stage IB acinar micropapillary No No No
75 14933 0.599 P Stage I Stage IA3 acinar micropapillary No Yes No
77 14955 0.560 P Stage II Stage IIB solid acinar No No No
81 15001 0.532 I Stage I Stage IB micropapillary acinar No No No
83 15083 0.421 I Stage I Stage IA2 acinar micropapillary, lepidic No No No
93 15741 0.405 I Stage I Stage IA2 acinar lepidic No No No

AGGRESSIVE as SILA > 0.6

pt_ID SILA CANARY Stages_simplified X8th_ed_path_stage Hist_predominant Hist_other_patterns Death_st Recurrence_st Progression_st
3 11424 0.750 P Stage I Stage IA3 solid NA No No No
5 11538 0.758 P Stage I Stage IB micropapillary NA No Yes No
7 11601 0.610 P Stage I Stage IA1 solid acinar No No No
8 11646 0.695 P Stage I Stage IA2 micropapillary solid, acinar No No No
11 11759 0.634 P Stage I Stage IA2 acinar micropapillary No No No
13 11817 0.797 P Stage II Stage IIB acinar solid Yes Yes Yes
14 11820 0.665 P Stage I Stage IA1 acinar solid No No No
17 11855 0.761 P Stage I Stage IA3 acinar NA No No No
19 11901 0.647 P Stage I Stage IA3 acinar solid Yes No No
23 11952 0.822 P Stage I Stage IA3 acinar NA No No No
24 11957 0.712 P Stage III Stage IIIA acinar solid Yes No No
25 12177 0.649 P Stage III Stage IIIA acinar solid Yes No Yes
27 12323 0.794 P Stage III Stage IIIA acinar micropapillary No No No
29 12889 0.768 P Stage II Stage IIB solid NA No No No
30 12890 0.791 P Stage II Stage IIA acinar micropapillary Yes No Yes
33 12924 0.669 P Stage II Stage IIB papillary acinar Yes Yes No
34 12929 0.622 P Stage II Stage IIB acinar lepidic Yes No Yes
35 12931 0.790 P Stage II Stage IIA solid acinar No No No
37 12994 0.750 P Stage III Stage IIIB micropapillary acinar Yes No Yes
38 13014 0.735 P Stage II Stage IIA acinar micropapillary No No No
41 13074 0.742 P Stage I Stage IA2 solid acinar Yes No Yes
42 13155 0.731 P Stage I Stage IA3 acinar micropappilary No No No
43 13197 0.697 P Stage II Stage IIB acinar micropapillary No No No
44 13207 0.675 P Stage I Stage IA3 micropapillary NA No No No
46 13317 0.697 P Stage I Stage IA3 micropapillary solid No No No
47 13356 0.621 P Stage II Stage IIB acinar solid Yes No No
49 13436 0.739 P Stage II Stage IIB acinar NA No No No
52 13579 0.664 P Stage II Stage IIB acinar NA No No No
53 13622 0.799 P Stage II Stage IIA solid NA No No No
55 13636 0.853 P Stage III Stage IIIA papillary NA No No No
57 13724 0.789 P Stage II Stage IIA solid acinar No Yes Yes
58 13746 0.821 P Stage IV Stage IV acinar NA No No Yes
59 13769 0.699 P Stage II Stage IIA acinar lepidic No No No
61 13774 0.735 P Stage I Stage IA3 acinar papillary Yes Yes Yes
62 13801 0.705 P Stage I Stage IA2 acinar NA Yes No No
65 14048 0.774 P Stage I Stage IB acinar NA Yes No No
67 14301 0.826 P Stage II Stage IIB micropapillary solid, acinar No No No
68 14330 0.732 P Stage II Stage IIA acinar lepidc No No No
70 14610 0.758 P Stage II Stage IIA mucinous acinar lepidic No No No
71 14813 0.627 P Stage I Stage IA2 solid acinar, lepidic No No No
73 14836 0.773 P Stage I Stage IA3 solid acinar No No No
76 14953 0.821 P Stage II Stage IIA solid NA No No No
79 14962 0.721 P Stage II Stage IIB papillary acinar No No No
82 15002 0.724 P Stage II Stage IIA solid NA No No No
84 15187 0.616 P Stage I Stage IA2 acinar lepidic No No No
85 15224 0.716 P Stage I Stage IA2 acinar papillary, micropapillary No No No
86 15325 0.622 P Stage I Stage IA1 papillary NA No No No
87 15326 0.612 P Stage I Stage IA3 acinar micropapillary No No No
88 15467 0.699 P Stage I Stage IA3 mucinous acinar NA No No No
89 15506 0.777 P Stage II Stage IIA mucinous acinar NA No No No
90 15569 0.687 P Stage II Stage IIA acinar solid No No No
91 15626 0.699 P Stage II Stage IIB acinar micropapilary, papillary, lepidic No No Yes 
## Using n_op1 as id variables

## Using n_op2 as id variables
## Warning in wilcox.test.default(c(0.049, 0.115, 0.23, 0.315, 0.36, 0.34, : cannot
## compute exact p-value with ties